Figure 1.
(Top) Histograms of the difference in allele signals (Col-0 allele probe – other allele probe) of sense strand signals between the Col-0 and Kr-0 parent arrays for probe sets marked by the Atwell et al. [12] as polymorphic (markers) and not marked as polymorphic (controls). (Bottom) Histograms of the allele signals from the parent arrays and the pseudo-F1 array constructed from the mean of the parent arrays. The pseudo-F1 array signals are distributed about zero, as would be expected for an actual heterozygous plant.
Figure 2.
100 simulations performed by selecting the extreme 10% of phenotypic variation for a population of 200 F2 plants with a major additive QTL at the 36th centimorgan on the second chromosome, shown in gray. The bold lines represent the average of the 100 simulations for each chromosome. The dashed horizontal orange and red lines represent the 95 and 99% confidence thresholds for detection, respectively, established by the 1000 permutation simulations displayed in Table 1. The black dashed vertical line represents the location of the simulated QTL, with the neighboring blue dashed lines representing the boundaries of the 18.5 cM wide confidence interval formulated from our simulations.
Table 1.
Results of simulations.
Figure 3.
A comparison of BSA with SFP genotyping vs. BSA with SNP genotyping using the same genomic DNA for hybridization. A. The dashed line represents the detection threshold of 0.17 established by Borevitz et al. [3]. B The dashed lines represent the 95 and 99% confidence thresholds for detection established by our simulations.